VMD is a powerful and flexible molecular visualization and analysis program, traditionally scriptable through Tcl. vmd-python provides a set of python 3 bindings for (most) VMD functions and subroutines. This package uses vmd-python to create automated movie productions for molecular trajectories through two steps:
- Individual frame manipulation and rendering through vmd-python commands
- Image collation/movie production through ImageMagick
All dependencies should be available through your favorite package manager.
- vmd-python 3.0+
- vmd
- numpy
- ImageMagick
- OpenCV 3.0+
git clone https://github.com/nec4/vmdviz/ .cd vmdvizpython setup.py install
For script info, run:
$ vmdviz_render -h
or
$ movie_combine -h
Molecular styles, scene, rendering, and movie production options are specified
in a runtime configuration file (created upon install at $HOME/.vmdvizrc.json).
This file is written in human-readable JSON, which is easily loaded as a python
dictionary.
VMD saves movies as a bunch of images and uses external software to collate
them into the final file. Here, we offer the flexibility for the user to use
their favorite CLI movie tool (eg,
ImageMagick,
ffmpeg, etc). For security
reasons,
actual collation of the image files rendered by VMD is decoupled from VMDviz.
For an example of post-processing, a BASH script tachyon_movie.sh is offered in
scripts/.
For help on a particular function/class, please run help(function/class), or
see docstrings in source.
- Expand rendering options (current default is Tachyon, bundled with VMD)
- Generalize rendering options in shell scripts
- Reorganize representation options